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Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery. / Behsaz, Bahar; Bode, Edna; Gurevich, Alexey; Shi, Yan Ni; Grundmann, Florian; Acharya, Deepa; Caraballo-Rodríguez, Andrés Mauricio; Bouslimani, Amina; Panitchpakdi, Morgan; Linck, Annabell; Guan, Changhui; Oh, Julia; Dorrestein, Pieter C.; Bode, Helge B.; Pevzner, Pavel A.; Mohimani, Hosein.

In: Nature Communications, Vol. 12, No. 1, 3225, 28.05.2021.

Research output: Contribution to journal › Article › peer-review

Harvard

Behsaz, B, Bode, E, Gurevich, A, Shi, YN, Grundmann, F, Acharya, D, Caraballo-Rodríguez, AM, Bouslimani, A, Panitchpakdi, M, Linck, A, Guan, C, Oh, J, Dorrestein, PC, Bode, HB, Pevzner, PA & Mohimani, H 2021, 'Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery', Nature Communications, vol. 12, no. 1, 3225. https://doi.org/10.1038/s41467-021-23502-4

APA

Behsaz, B., Bode, E., Gurevich, A., Shi, Y. N., Grundmann, F., Acharya, D., Caraballo-Rodríguez, A. M., Bouslimani, A., Panitchpakdi, M., Linck, A., Guan, C., Oh, J., Dorrestein, P. C., Bode, H. B., Pevzner, P. A., & Mohimani, H. (2021). Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery. Nature Communications, 12(1), [3225]. https://doi.org/10.1038/s41467-021-23502-4

Vancouver

Behsaz B, Bode E, Gurevich A, Shi YN, Grundmann F, Acharya D et al. Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery. Nature Communications. 2021 May 28;12(1). 3225. https://doi.org/10.1038/s41467-021-23502-4

Author

Behsaz, Bahar ; Bode, Edna ; Gurevich, Alexey ; Shi, Yan Ni ; Grundmann, Florian ; Acharya, Deepa ; Caraballo-Rodríguez, Andrés Mauricio ; Bouslimani, Amina ; Panitchpakdi, Morgan ; Linck, Annabell ; Guan, Changhui ; Oh, Julia ; Dorrestein, Pieter C. ; Bode, Helge B. ; Pevzner, Pavel A. ; Mohimani, Hosein. / Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery. In: Nature Communications. 2021 ; Vol. 12, No. 1.

BibTeX

@article{e6fc9c44836a4f438288f564283fa1d0,
title = "Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery",
abstract = "Non-Ribosomal Peptides (NRPs) represent a biomedically important class of natural products that include a multitude of antibiotics and other clinically used drugs. NRPs are not directly encoded in the genome but are instead produced by metabolic pathways encoded by biosynthetic gene clusters (BGCs). Since the existing genome mining tools predict many putative NRPs synthesized by a given BGC, it remains unclear which of these putative NRPs are correct and how to identify post-assembly modifications of amino acids in these NRPs in a blind mode, without knowing which modifications exist in the sample. To address this challenge, here we report NRPminer, a modification-tolerant tool for NRP discovery from large (meta)genomic and mass spectrometry datasets. We show that NRPminer is able to identify many NRPs from different environments, including four previously unreported NRP families from soil-associated microbes and NRPs from human microbiota. Furthermore, in this work we demonstrate the anti-parasitic activities and the structure of two of these NRP families using direct bioactivity screening and nuclear magnetic resonance spectrometry, illustrating the power of NRPminer for discovering bioactive NRPs.",
keywords = "Algorithms, Amino Acid Sequence/genetics, Anti-Bacterial Agents/biosynthesis, Biological Products/isolation & purification, Computational Biology/methods, Datasets as Topic, Drug Discovery/methods, Humans, Mass Spectrometry, Metabolic Networks and Pathways/genetics, Metabolomics/methods, Metagenomics/methods, Microbiota/genetics, Multigene Family, Peptide Biosynthesis, Peptide Synthases/genetics, Peptides/genetics, Soil Microbiology, DRUG DISCOVERY, MASS-SPECTROMETRY, BIOSYNTHETIC GENE CLUSTERS, SURFACTIN, DIVERSITY, ADENYLATION DOMAINS, NATURAL-PRODUCTS, IDENTIFICATION, DATABASE SEARCH, BACILLUS-SUBTILIS",
author = "Bahar Behsaz and Edna Bode and Alexey Gurevich and Shi, {Yan Ni} and Florian Grundmann and Deepa Acharya and Caraballo-Rodr{\'i}guez, {Andr{\'e}s Mauricio} and Amina Bouslimani and Morgan Panitchpakdi and Annabell Linck and Changhui Guan and Julia Oh and Dorrestein, {Pieter C.} and Bode, {Helge B.} and Pevzner, {Pavel A.} and Hosein Mohimani",
note = "Publisher Copyright: {\textcopyright} 2021, The Author(s).",
year = "2021",
month = may,
day = "28",
doi = "10.1038/s41467-021-23502-4",
language = "English",
volume = "12",
journal = "Nature Communications",
issn = "2041-1723",
publisher = "Nature Publishing Group",
number = "1",

}

RIS

TY - JOUR

T1 - Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery

AU - Behsaz, Bahar

AU - Bode, Edna

AU - Gurevich, Alexey

AU - Shi, Yan Ni

AU - Grundmann, Florian

AU - Acharya, Deepa

AU - Caraballo-Rodríguez, Andrés Mauricio

AU - Bouslimani, Amina

AU - Panitchpakdi, Morgan

AU - Linck, Annabell

AU - Guan, Changhui

AU - Oh, Julia

AU - Dorrestein, Pieter C.

AU - Bode, Helge B.

AU - Pevzner, Pavel A.

AU - Mohimani, Hosein

N1 - Publisher Copyright: © 2021, The Author(s).

PY - 2021/5/28

Y1 - 2021/5/28

N2 - Non-Ribosomal Peptides (NRPs) represent a biomedically important class of natural products that include a multitude of antibiotics and other clinically used drugs. NRPs are not directly encoded in the genome but are instead produced by metabolic pathways encoded by biosynthetic gene clusters (BGCs). Since the existing genome mining tools predict many putative NRPs synthesized by a given BGC, it remains unclear which of these putative NRPs are correct and how to identify post-assembly modifications of amino acids in these NRPs in a blind mode, without knowing which modifications exist in the sample. To address this challenge, here we report NRPminer, a modification-tolerant tool for NRP discovery from large (meta)genomic and mass spectrometry datasets. We show that NRPminer is able to identify many NRPs from different environments, including four previously unreported NRP families from soil-associated microbes and NRPs from human microbiota. Furthermore, in this work we demonstrate the anti-parasitic activities and the structure of two of these NRP families using direct bioactivity screening and nuclear magnetic resonance spectrometry, illustrating the power of NRPminer for discovering bioactive NRPs.

AB - Non-Ribosomal Peptides (NRPs) represent a biomedically important class of natural products that include a multitude of antibiotics and other clinically used drugs. NRPs are not directly encoded in the genome but are instead produced by metabolic pathways encoded by biosynthetic gene clusters (BGCs). Since the existing genome mining tools predict many putative NRPs synthesized by a given BGC, it remains unclear which of these putative NRPs are correct and how to identify post-assembly modifications of amino acids in these NRPs in a blind mode, without knowing which modifications exist in the sample. To address this challenge, here we report NRPminer, a modification-tolerant tool for NRP discovery from large (meta)genomic and mass spectrometry datasets. We show that NRPminer is able to identify many NRPs from different environments, including four previously unreported NRP families from soil-associated microbes and NRPs from human microbiota. Furthermore, in this work we demonstrate the anti-parasitic activities and the structure of two of these NRP families using direct bioactivity screening and nuclear magnetic resonance spectrometry, illustrating the power of NRPminer for discovering bioactive NRPs.

KW - Algorithms

KW - Amino Acid Sequence/genetics

KW - Anti-Bacterial Agents/biosynthesis

KW - Biological Products/isolation & purification

KW - Computational Biology/methods

KW - Datasets as Topic

KW - Drug Discovery/methods

KW - Humans

KW - Mass Spectrometry

KW - Metabolic Networks and Pathways/genetics

KW - Metabolomics/methods

KW - Metagenomics/methods

KW - Microbiota/genetics

KW - Multigene Family

KW - Peptide Biosynthesis

KW - Peptide Synthases/genetics

KW - Peptides/genetics

KW - Soil Microbiology

KW - DRUG DISCOVERY

KW - MASS-SPECTROMETRY

KW - BIOSYNTHETIC GENE CLUSTERS

KW - SURFACTIN

KW - DIVERSITY

KW - ADENYLATION DOMAINS

KW - NATURAL-PRODUCTS

KW - IDENTIFICATION

KW - DATABASE SEARCH

KW - BACILLUS-SUBTILIS

UR - http://www.scopus.com/inward/record.url?scp=85106994191&partnerID=8YFLogxK

UR - https://www.mendeley.com/catalogue/c0a033f7-873b-31a4-a088-24e7d2e90f24/

U2 - 10.1038/s41467-021-23502-4

DO - 10.1038/s41467-021-23502-4

M3 - Article

C2 - 34050176

AN - SCOPUS:85106994191

VL - 12

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

IS - 1

M1 - 3225

ER -

ID: 84851795